[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-18-g2f459ff

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit d374b906850002f364610c535789e2bc85b1fd12
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Wed May 9 14:10:45 2012 +0200

    added patch fixing #672090
    updated DEP3 headers
    bumperd Standards-Version to 3.9.3

diff --git a/debian/control b/debian/control
index 03a5e16..d1dc29d 100644
--- a/debian/control
+++ b/debian/control
@@ -6,7 +6,7 @@ DM-Upload-Allowed: yes
 Uploaders: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>,
  Andreas Tille <tille at debian.org>
 Build-Depends: debhelper (>= 8.0), help2man
-Standards-Version: 3.9.2
+Standards-Version: 3.9.3
 Homepage: http://bowtie-bio.sourceforge.net/bowtie2
 Vcs-Browser: http://git.debian.org/?p=debian-med/bowtie2.git
 Vcs-Git: git://git.debian.org/debian-med/bowtie2.git
diff --git a/debian/patches/bowtie2_gcc4.7.patch b/debian/patches/bowtie2_gcc4.7.patch
new file mode 100644
index 0000000..8ed75d8
--- /dev/null
+++ b/debian/patches/bowtie2_gcc4.7.patch
@@ -0,0 +1,14 @@
+Description: porting to gcc4.7 added include <unistd.h>
+Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
+Last-Update: 2012-05-09
+
+--- bowtie2.orig/word_io.h
++++ bowtie2/word_io.h
+@@ -20,6 +20,7 @@
+ #ifndef WORD_IO_H_
+ #define WORD_IO_H_
+ 
++#include <unistd.h>
+ #include <stdint.h>
+ #include <iostream>
+ #include <fstream>
diff --git a/debian/patches/fix_makefile_machine_detection.patch b/debian/patches/fix_makefile_machine_detection.patch
index 050ba38..864cad7 100644
--- a/debian/patches/fix_makefile_machine_detection.patch
+++ b/debian/patches/fix_makefile_machine_detection.patch
@@ -1,7 +1,7 @@
 Subject: Attemp to adapt build flags to built package on all supported 
  architectures.
 Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Date: 2012-03-10
+Date: 2012-05-09
 --- bowtie2.orig/Makefile
 +++ bowtie2/Makefile
 @@ -107,20 +107,33 @@
diff --git a/debian/patches/series b/debian/patches/series
index bc60eae..feb5f36 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
+bowtie2_gcc4.7.patch
 fix_makefile_machine_detection.patch

-- 
ultrafast memory-efficient short read aligner